Role of Agricultural Management in the Provision of Ecosystem Services in Warm Climate Vineyards: Functional Prediction of Genes Involved in Nutrient Cycling and Carbon Sequestration

Abstract

(1) Background: Maintaining soil fertility and crop productivity using natural microbial diversity could be a feasible approach for achieving sustainable development in agriculture. In this study, we compared soils from vineyards under organic and conventional management by predicting functional profiles through metagenomic analysis based on the 16S rRNA gene. (2) Methods: The structure, diversity and predictive functions of soil bacteria related to the biogeochemical cycle of the soil were analyzed, including oxidative and hydrolytic C-cycling enzymes, N-cycling enzymes and P-cycling enzymes. The inter-row spontaneous vegetation in the organic vineyards was also characterized. (3) Results: A clear effect of the farming system (organic vs. conventional) and cover management (herbicides plus tillage, mowing only and mowing plus tillage) on bacterial beta diversity and predicted functions was evidenced. While conventional viticulture increased the potential capacity of the soil to regulate the cycling of inorganic forms of N, organic viticulture in general enhanced those functions involving organic N, P and C substrates. Although the soil bacterial community responded differently to contrasting soil management strategies, nutrient cycling and carbon sequestration functions remained preserved, suggesting a high bacterial functional redundancy in the soil in any case. However, most of the predicted bacterial functions related to soil organic matter turnover were enhanced by organic management. (4) Conclusions: We posit the potential for organic viticulture to adequately address climate change adaptation in the context of sustainable agriculture.

Keywords: cover vegetation; ecosystem functions; nutrient cycling; soil bacteria; vineyard.

Figure 1

Relative abundance of soil bacteria in conventional and organic vineyards.

Figure 2

Linear discriminant analysis (LDA) scores and heatmap from blue (low) via white (medium) to red (high) of relative abundances in (A) conventional (C) and organic (O) systems and, (B) herbicide + tillage (H + T), mowing only (M) and mowing + tillage (M + T) cover managements.

Figure 3

Effect of farming (A) and cover management (B) on bacterial beta diversity in vineyards’ soils. Ordination method PCoA; distance method: Bray-Curtis index; statistical method: PERMANOVA. Ellipses mean that 95% of the data fell inside the ellipse.

Figure 4

KEGG pathway molecular functions of nitrogen cycle for soils under conventional (yellow) and organic (green) management. Asterisk represents a significant difference (** p < 0.01).

Figure 5

KEGG pathway molecular functions of organic phosphorus cycle for soils under conventional (yellow) and organic (green) management. phoN: acid phosphatase (class A) [EC 3.1.3.2]; PHO: acid phosphatase [EC 3.1.3.2]; phoA,B: alkaline phosphatase [EC 3.1.3.1]; phoD: alkaline phosphatase [EC 3.1.3.1]. Asterisk represents a significant difference (** p < 0.01, * p < 0.05).

Figure 6

KEGG molecular functions of genes encoding carbon hydrolases in soils under conventional (yellow) and organic (green) management. NAG: mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase [EC 3.2.1.96]; xynB: xylan 1,4-beta-xylosidase [EC 3.2.1.37]; β-Glucanase: 3-beta-D-glucan glucohydrolase [EC 3.2.1.58]; CBH1: cellulose 1,4-beta-cellobiosidase [EC 3.2.1.91]; β-glucosidase [EC 3.2.1.21]. Asterisk represents a significant difference (** p < 0.01, * p < 0.05).

Figure 7

KEGG pathway molecular functions of carbon oxidoreductases for soils under conventional (yellow) and organic (green) management. pmo NADPH: phenol 2-monooxygenase (NADPH) [EC 1.14.13.7]; pmo NADH: phenol 2-monooxygenase (NADH) [EC 1.14.13.244]; katG: catalase-peroxidase [EC 1.11.1.21]; npr: NADH peroxidase [EC 1.11.1.1]; tfdB: 2,4-dichlorophenol 6-monooxygenase [EC 1.14.13.20]; tmo: toluene monooxygenase system protein [EC 1.14.13.236]. Asterisk represents a significant difference (** p < 0.01, * p < 0.05).

Figure 8

KEGG pathway molecular functions of carbon fixation for soils under conventional (yellow) and organic (green) management. CBB: Calvin-Benson-Bassham cycle; cbbL: ribulose-bisphosphate carboxylase [EC 4.1.1.39]. Asterisk represents a significant difference (** p < 0.01, * p < 0.05).

Figure 9

NMDS plot showing mean position of each bacterial KEGG KO according to cover management practices (herbicide, tillage, mowing) as dissimilarity vectors. Each point represents a vineyard sample: conventional (yellow) and organic (green) management. Vector significance: herbicide R² = 0.636, p-value = 0.001; tillage R² = 0.430, p-value = 0.018; mowing R² = 0.636, p-value = 0.001. Management (conventional, organic) significance: R² = 0.577, p-value = 0.001. Stress = 0.006.